Ministers have insisted that the authorities are doing "everything possible" to protect homes from flooding as the UK braced for further heavy rain and gales.

The military was on stand-by across southern Britain should troops be required to help as the Government stepped up efforts to tackle the problem.

Following a meeting of the Government's emergency Cobra committee, Communities Secretary Eric Pickles warned the "worst of the bad weather is not over" but insisted the authorities were working "tirelessly" on the flooding crisis.

With David Cameron visiting flood-hit areas of the south west, Mr Pickles chaired the meeting, which came as communities along the River Thames and in Somerset were warned to expect more flooding into tomorrow as river levels continue to rise.

The Communities Secretary said: " As we continue to face these extraordinary weather events, I want to make clear again this evening that work is being done to identify and prioritise any sites where we may experience problems in the coming days.

"I want to reassure the public that their safety remains our first priority. We are doing everything possible to protect people's homes and communities. In addition, strategic sites such as water and electrical plants are being given special attention to ensure that homes are not left without vital resources

"Local Authorities are being given immediate practical support from Government. This includes centralising the control of sandbags, ordering additional temporary flood defences and ensuring that existing defences are being shared and deployed where necessary.

"Additionally, full military support remains on stand by across the south.

"Network Rail are working on a plan to reconnect the affected rail line to the south west. However, two out of the three rail routes to Exeter are now open.

"Sadly, the worst of the bad weather is not over. But we are working tirelessly to deal with the situation on the ground and to prepare and protect vulnerable areas"

Mr Pickles found himself at the centre of a row following barbed comments about the Environment Agency (EA), with the quango hitting back at "ill-informed and unfair" criticism.

EA board members suggested that the dispute was "undermining" public confidence and "belittling" the work of staff working hard to minimise the impact of extreme weather.

The EA said it acknowledged that a debate about dredging was needed and sympathised with the anger felt by flood victims, but claimed that its work was based on "firm evidence and tested science".

" Of course it is open to anyone to take issue with expert scientific opinion," the agency's independent board members said in a statement.

"But at a time of emergency it is more important for us all to focus relentlessly on managing the current floods and helping to minimise their impact.

"Just as it is wrong to criticise the work of our staff on the ground, it is equally wrong to seek to place blame for the recent flooding events on the chairman and 'people in London'."

The Thames Valley is expected to bear the brunt of the storms this week. Forecasters have said there is little chance of the weather easing until at least next week.

EA chairman Lord Smith said his staff and the Army were helping residents in flood-hit Wraysbury in Berkshire as he issued a fresh defence of how his organisation had responded to the Thames flooding.

He told Channel 4 News: "All the necessary warnings were put in place. We told everyone what was likely to happen.

"Our staff have been out helping in many different parts of the Thames Valley, we were assisting in Datchet last night. I'm told that our staff will be going in, together with the Army to Wraysbury this evening to help there."

Efforts to deal with the flooding have been overshadowed by a bitter clash between ministers and the EA, after Mr Pickles yesterday issued an apology for relying on its advice.

Environment Secretary Owen Paterson - who was leading the response until being forced to undergo an eye operation - is said to have complained to Downing Street over his Tory colleague's intervention.

Mr Pickles sought to make light of a supposed rift, describing Mr Paterson as his "brother from a different mother" after being summoned to the Commons to respond to an urgent question.

Attempting to take the heat out of the spat this afternoon, the Prime Minister said: "I am only interested in one thing, and that is making sure that everything government can do is being done, and will go on being done to help people through this difficult time."

Asked whether Mr Cameron agreed with an unnamed Cabinet minister who was quoted as describing Mr Paterson as "stupid", his spokesman responded: "The Prime Minister's view is that Owen Paterson does an excellent job."

Labour leader Ed Miliband said: "It is a disgrace that you have Government ministers today pointing the finger at each other when they should be rolling their sleeves up and helping those who are affected.

"The Government needs to explain why their response to the flooding has been so slow to help the victims and why their planning has been so inadequate.

The Met Office's Sarah Davies told a briefing that strong winds forecast for the middle of the week could add to the problems facing the country.

Some 20-40mm (0.75-1.5 inches) of rain is expected by Friday night across many southern and western areas.

But some regions, including the already flood-hit south west of England, south Wales, western Scotland and Northern Ireland could have up to 70mm (2.75 inches).

The EA's Pete Fox said up to 900 homes had been flooded since the end of last week and added: " You might expect to see some hundreds of properties flooded over the course of the next two or three days."

Network Rail said disruption to lines and infrastructure could take "some months" to resolve.

Chancellor George Osborne said the flooding would lead to a debate about how to manage the countryside.

He told ITV's The Agenda : "I think people understand that the rain is not the fault of any one person. But how we as a country cope with that, of course that is a responsibility for people like me."

Mr Osborne defended the funding available to tackle the crisis: " We're investing in the frontline services now to get these rail lines repaired, to protect homes along the Thames at the moment, the homes in Somerset, bring in the Army and all that kind of thing.

"It does lead to a real debate about how we look after our countryside."

Lord Smith acknowledged mistakes had been made but blamed Treasury funding rules and the failure to get funding from local authorities in Somerset for the lack of dredging on the Levels' rivers.

On BBC 2's Newsnight he added: "We've all made mistakes, everyone has made mistakes. The Environment Agency has done a really good job of protecting 1.3 million homes over the course of the last two months that would have been flooded if our defences hadn't been in place.

"There are things like last year, on the Somerset Levels, when we put £400,000 on the table to start some real dredging on the Tone and the Parrett. That was the maximum we were allowed to spend by the Treasury rules that bind us.

"What we didn't do and we should probably have done was to really twist arms of the other players, the district councils, the county council, the drainage boards to come to the table with other contributions in order to enable us to do that ... It was something that we all should have worked more actively on."

Asked who was to blame for the floods he said: "Fundamentally it's the weather's fault. We have had the most extreme weather over the course of the last two or three months that we have ever seen.

"The highest storm surge on the east coast for 60 years, the stormiest period over Christmas and the New Year, the wettest January ever recorded, the highest waves ever recorded against the south coast.

"This is extreme natural forces having a go at us and we need to find the best possible ways of defending ourselves against them."

Acknowledging that in some places land would have to be given up to the forces of nature he said: "I don't think there's anywhere where there is a community, where there's economic activity or where there's vibrant life going on, I don't think there is anywhere that we should simply give up on."

But he added: "There will be some areas of land, some areas of coast where we probably, in due course - not immediately but in due course - we probably need to retreat a little bit in order to protect better."